If you look at other genres that have superpowers and observe their sources, it may give you a better idea of how you can categorize those sources in the world you're building.
Innate: Starting with the basic, these powers are there from birth. Examples include Superman (Kryptonian DNA) and sorcerers from Dungeons and Dragons (magic is in their blood).
Bestowed: These powers are given by someone greater, usually with an agreement that they be used in a particular way. Examples include Wonder Woman (Aphrodite's Law) and D&D clerics (powers granted by their gods).
Cursed: These powers are much like the bestowed powers, except they come from some kind of calamity. Examples include almost all super villains it seems like, Spider-Man (spider bite) and the Fantastic Four (cosmic radiation).
Independent Object: Sometimes the powers aren't within the user, but within particular items that the user wields. Examples include Green Lantern (his ring) and D&D wizards (spellbooks/spells).
I think that sums it up. So an attempt at translating them to your world:
Innate powers would be powers that the players gain through being themselves and leveling up. So those would be part of their proper programming. Bestowed powers would be the "special privileges" granted by the God AI. Cursed powers would be the result of your "glitches" -- something happens that wasn't supposed to, and as a result, a (probably temporary, unpredictable, or watered-down) power is granted. Independent objects be anything that the user wields in-game, including weapons, scrolls, potions, armor... and I personally believe your "hacker tools" falls here.
As a side-note, it might be pretty interesting to see what happens when, once the players are comfortable in their world, a real-life human begins messing with the program. Rearranging code, changing variables, etc -- A conscious choice made by the creator of the program (you) in an effort to somehow "improve" the gameplay experience.
is my list complete? or are there any other points that could be added to it?
I think it's a pretty complete list. You've covered most of the tropes surrounding power sources.